Tail of the Ancient Tides
by WraithLoverQueen
Summary: A strange creature has gotten past Atlantian shields and is loose in the ancient city but now it's after doctor Mckay. Awkward for Rodney and pain  both physical and emotional  for John follows. No slash, just REALLY close friendships that feel like slash
1. Chapter 1

A/N: A season 1 AU. Why? Because I've only seen the first 9 episodes, that's why. I hope you guys like it. ^^ It gets a little weird, but I guess people expect that from Stargate fics. Also, characters might be a little OOC, I'm still getting to know them. So, please bare with me. ^^

Tail of the Ancient Tides

Chapter 1

The violet moonlight cascaded through the highest most blood-stain room of the ominous citadel of Ovara, a desolate world of icy swamps and bogs. A tall woman with flowing crimson hair sat upon a pointed ebony throne with a dark haired man sitting on the floor next to her.

"Mistress Thuqua?" The crimson-haired woman turned her head at the sound of her name and smirked slightly.

"Wuna, is it open yet? He's ready." Thuqua asked softly as she gently reached down to scratch the man's chin and the rub her hand up and down his throat like you would a pet, making the dark-haired man purr happily. Wuna watched the scene with slight disgust before clearing her throat, "Yes, Mistress, the stargate is practically open. With his help we can get past the shields with a bit of tweaking but are you sure he's ready? We've only had him a month, it usually takes longer!"

"Wuna, you worry too much. This man's mind was trained to have have orders and the like forced into it. With any previous relations washed away, we have put new relations in. He works for us now." Thuqua stood up and started to walk towards the younger girl, leaving the man sitting on the icy marble floor.

"Bur Mistress, what if he's there and he get flashes of recognition!"

"If he does, the drug will kick in. Taking any memory he has of them and twisting it so that he believes they are who put him through that month of pain and suffering. He'll have no clue that he's even betraying his own people..." Thuqua whispered so that only Wuna would hear before turning back to the man, "Jay, come 'ere, boy." With stood up but was still slightly crouched and walked over to them then sat down in front of the crimson-haired woman, smiling up at her like she was his best friend.

"Mistress, are you sure we should be doing this? It feels wrong!" Wuna exclaimed as Thuqua reached down to scratch Jay behind the ear.

"Science, my dear..."

"Excuse me?"

"Science. This is all for the good of science, the world would be nothing without it." Thuqua informed then turned to look at Jay, "Jay, this is a brilliant scientist by the name of Rodney Mckay. You are to go and fetch him for me, ok?" The dark-haired man nodded happily before panting slightly, making Wuna's stomach flip in disgust for what she had help resort a once defiant man down to while Thuqua continued.

"Get him by any means necessary. He can be a little banged up but not too much and if anyone gets in between you and the good doctor, then kill them." Jay nodded again as his mistress motioned for Wuna to take him away and send him through the portal before she walked away. Wuna, still utterly disgusted with herself, pulled a black leather leash out of her lab coat pocket and clipped it to the leather ID collar that Jay wore. She walked towards the door, muttering, as he trail behind; ever happy to be of service.

They continued down the many corridors, the sick feeling never leaving Wuna as they finally got to the stargate. She stopped and stared down at Jay, who was sitting in a cross legged position next to her, eager for attention. Bending down towards him, her took his head in her hands and stared into his eyes.

"I am so sorry, sir... I'll try to put this right, I swear. Don't worry, I'll fix you and you can go back to living your life with your friends." Jay didn't seem to comprehend what she had said to but could tell that she was upset. Whimpering slightly, he craned his neck upward then licked across the top of her nose and the bridge of her glasses; making tears drip from her eyes at how far this once great man had fallen. Forcing herself to stand up straight, she typed in the code for the stargate and unclipped Jay's leash. The dark-haired man stood and cocked his head to the side before rushing through the portal. Wuna sighed and help back anymore tears of sympathy and sorrow, she had work to do; she needed to get started on the reversal project.

~S~G~A~

Alarms blared as Jay arrived in Atlantis but before any of the guards could get a good look at him or get a shot off, he was using hands and feet to scramble towards the shadows. He needed to find that doctor, he wondered what he looked like. Hiding behind some near by crates, he heard a woman and a young man talking.

"Lieutenant, what happened."

"Something slipped through the shield but we didn't a glimpse of what it was."

"It could be dangerous. Find it quick!"

"Yes, ma'am." Jay didn't have time to sit around and listen to them all day. So staying to the shadows, he creeped along the corridors of Atlantis. His bare feet oddly silent along the hard ground and he turned a few more corners before worming his way into a nearby room. It was currently empty but seemed to be some sort of command room. His animal thoughts pushed back just for the human ones to come forward, Jay stood up tall and started to look about. It took a good ten minutes for his brain to find and register a book full of department listings; he quickly flipped through a few pages until he found Mckay's name and workstation listed. Committing it to memory, he snapped the book closed and turned to leave. He was greeted by a shocked gasp of a guard that had been patrolling but before the guard could say anything, Jay had leaped at him; smacking the younger man to the ground.

"Stop it, sir!" The guard squeaked as Jay slammed a fist into his then hissed as the young man tried to shove him off but Jay wouldn't budge, instead grew tired of his opponent and simply used his claw-like nails to rip the man's throat open; blood spraying up the man's slice jugular. Jay sprang to his feet and rushed for the door, leaving the guard to die. Licking the blood from his nails as he ran, an unfamiliar instinct took over and began leading him towards the labs when Rodney Mckay was supposed to be stationed. Along the way, he ran into two more guards; killing them with trained ease.

It was about ten minutes later, skidded to a halt in the deserted hallway in front of the lab and simply panted for breath. Suddenly, the door opened for him, spooking him slightly. Cautiously, he stepped inside, it had to be night in Atlantis from the way that their was only one person sitting at one of the lab tables. An uncomfortable vibe inside Jay told him that it wasn't Mckay but might know where he is, his human instincts said he should take this one hostage. Moving slowly, he used his bare feet to creep silently up on his prey until he was behind the ponytailed scientist.

~S~G~A~

It was late at night but with the threat of a monster running around in Atlantis made it impossible for Doctor Kavanagh to sleep, so he had decided to simply continue his work on the ancient crystal the recon team had picked up on their last missions. He was completely alone in the lab beside that annoying doctor Mckay in the next room, at least the door was closed between their two work areas. All was quiet until he heard the door to the lab open, he didn't turn around since the only explanation was that Rodney was off to go get a midnight snack or at least that's what he thought until he saw slow movement behind him in the reflection of a beaker. Thoughts of the creature entered his head as the thing behind him creeped closer silently. Not being a nature fighter but sill wanting to protect himself from attack, Kavanagh slowly grabbed the closest thing to him that was sharp; the crystal he had been working on. Then, jest as the thing rushed to attack him, he span around in his chair and blindly stabbed the crystal into his attacker before looking up to see what it was.

"M-major S-sheppard...?" Kavanagh paled as realization hit while the major stumbled backwards and collapsed to his knees. Mind hazy with confusion, Kavanagh did the first thing that came to mind, " DOCTOR MCKAY!"

~S~G~A~

Rodney sat in his lab chair, staring blankly at his files. He was so tired yet too depressed and worried to sleep, so forcing his body to work was the only thing he could think of but now even that was gone. Major Sheppard had been missing on that dreadful planet for little over a month now and it was eating away at Rodney, Teyla and Ford's sanity that he had gone MIA while trying to protect them from swamp monsters. Rodney's drooped until his forehead thunked against the hard metal table.

"Where in the name of science could he be!" He was far too tired to think up a better question as he whispered the words to the table. His eyes started to close as sleep began to overtake him and that's when he heard it!

"DOCTOR MCKAY!" The scream was frantic and scared but Rodney didn't hear that, he only heard an extremely annoying man call his name. Blood pumping angrily, he shot up from his chair and stormed for the door; wrenching it open.

"Kavanagh, what in the h-!" His works were cut off by his shock of the scene before him; a horrified looking Kavanagh standing before a scared looking John Sheppard who seemed to fall to his knees in slow motion. For once speechless, Rodney rushed over to them as the frightened looking Sheppard put a hand to his side and crawled backwards under a desk so he was still facing the two scientists. Cheeks flushed red with anger, Rodney glared at Kavanagh.

"What the heck did you do to him!" He didn't wait for a reply before dropping to his own knees to get a better look at the major. He stopped breathing at the sight of pure frozen horror in his commander's glassy looking eyes and the growing blood stain of where the crystal had pierced his abdomen.

"Kavanagh, quit gawking and call Beckett, quick!" This being said, Rodney reached out a shaky hand towards John, who only seemed to cower back as far as he could into the desk's empty leg room. The major looked utterly terrified of him and let out a pathetic whimper which broke Mckay's heart but he still reached for him; it wasn't until a long tail-like tendril slipped out of the major's baggy pants and slapped his hand away that he stop.

"Oh god, John, what did they do to you...?" Rodney's throat felt so dry with horror at what just happened that he could barely whisper out the words while looking at the tendril stand guard in front of the cowering major.

~~~~~~A/N: Cruddy, I know. But still, hope you guys enjoyed it. Please R&R, it helps me continue. ^^'


	2. Chapter 2

A/N: Tada! Chapter 2.

Chapter 2

Despite all his genius, Rodney's brain was drawing a blank; he had no idea how to help the major. He felt sick just looking at the other man cowering up the desk, Rodney didn't like how pale and thin he looked; like he hadn't been fed a healthy amount of food the entire the month he was gone. Suddenly, Rodney's stomach did a flip as John started to cough; his body's way of expelling the blood that was seeping into his vital organs through the puncture wound. Rodney had to stop his body from reaching out to the now panicking major so that he wouldn't spook him anymore, he needed to try a different tactic to get his friend's mind off the blood that his lungs were forcing up.

"Shhh... Shep, it's gonna be ok... Just calm down.." Rodney tried to sound encouraging to get the major, who was currently gripping at the wound and clawing at the wall, to calm down. Suddenly, Rodney realized that he hadn't heard Kavanagh's voice since he called him. The scientist turned around slightly to look at his annoying co-worker to see him frozen in place with shock.

"Kavanagh! Did you called Carson yet! We need him!" The scientist only got a frantic shake of the head in reply, which made his own panic heighten. Though oddly, Rodney, the master at panicking and over reacting, was the calmest one in the room but not by much.

"If you want something done right then you gotta do it yourself!" Fumbling to try and sooth his frightened friend, Rodney quickly activated his comlink, "Carson, come in! I'm in urgent need of medical assistance!"

~S~G~A~

Dr. Carson Beckett sat at the briefing table with Dr. Weir and Teyla, the three were discussing yet another failure to find Major Sheppard.

"So, doctor, what're your thoughts? Think he could still be alive?" Weir asked, sounding tired and slightly depressed. Carson sighed and shook his hanging head.

"Nay. From what Teyla 'as told meh, I donae think he could 'ave survived fer so long on a hostile world that's made of icy marshlands..." The three fell silent and depressed looking as the weight of the facts set in but the mood was abruptly disturbed by a radio transmission to Dr. Beckett.

_"Carson, Come in! I'm in urgent need of medical assistance!"_ Carson's eyes flew open at the sound of panic in the scientist's voice.

"Beckett 'ere, what's wrong, laddie...?"

_"This idiot Kavanagh was supposed to call you like five minutes ago! Holy Smoke, it's been five minutes! No wonder he's coughing up blood already!"_

'Did 'e realeh just say "Holy smoke"?' Carson mentally asked himself before the rest of what Mckay just said sank into his brain, "Who's coughin' up blood, Rodney? Kavanagh...?" Carson was already halfway to the door.

_"No, that idiot's gawking like a moron instead of helping me! It's Major Sheppard, he's back and Kavanagh just stabbed him with a crystal! He claims he didn't mean it..."_ Carson stopped dead in his tracks.

"The major...? Are you sure?" This made Weir and Teyla perk up in curiosity but before they both tuned their headsets to get Rodney's call.

"Rodney, it's Elizabeth, what was that about the major?"

_"He's here and bleeding! I don't have time for stupid questions just get Beckett to my lab as fast as you can!"_

"We're on our way thar, laddie. By aneh chance, can yeh apply pressure to teh major's wound?"

_"Pfft! No! Last time I even tried to touch him he slapped my hand away with his tail!"_

"His what!" The asked in unison as they all broke into a run down the hall.

_"It's a long story that I don't have answers to! All I know is that he's cowering under a desk in my lab and there's this weird tail-like thing coming out of his pant-leg that seems to be subconsciously guarding him from me!"_ By now, the three had picked up Beckett's medical bag and were almost to the lab; it all went faster than they thought it would have.

"Doctor Mckay, why is he cowering under a desk?" Teyla asked as they rounded another corner.

_"Look, I have no idea but as soon as he saw me he panicked and hid himself as best he could under the desk! Are you almost here yet!"_

"Yes, Rodney, we're right out side the door."

_"Oh goody, now hurry up!"_ The three sighed as the door opened and they rushed inside, running over to where they saw Rodney kneeling on the floor in front of a large desk with Kavanagh just sitting in a chair behind him. As they approached, Rodney held up a hand to make them stop before he pushed Kavanagh out of the way to make room for Teyla and the doctors. The three newcomers slowly dropped to their knees to look under the desk and sure enough, there sat a cowering Major John Sheppard with a strange tail sticking out of his pants just like Mckay said. Carson winced at the amount of blood had seeped onto the floor and staining the major's clothing.

"We 'ave teh get him out of thar so I can treat 'im." Rodney and Teyla nodded, it would have to be them that grabbed him and pull him out of his hiding spot. Doctor Weir watched silently as the two slowly reached for the panicked major when suddenly there was an incoming transmission to her.

_"Doctor Weir, it's Ford."_

"Yes lieutenant, go ahead."

_"There's an urgent transmission from Ovara."_ At the name of the planet, Elizabeth looked over at where John was struggling against his friends and shuddered.

"Let it through."

_"Yes, ma'am."_

_"Hello...?"_

"Greetings, my name is Doctor Elizabeth Weir, who're you?"

_"My name is Wuna of Ovara Citadal, I have urgent news for your leader!"_

"It's alright, Wuna, I'm in charge. Go ahead."

_"Alright. I only have limited time so here goes. About a month ago, your military personal, Major John Sheppard was captured by my mistress' trackers. During his stay in the citadel, we lived up to our title of Beast Makers. We preformed countless horrifying and torturous experiments on him,"_ Weir felt like she was going to be sick, _"I won't bore you with details of them but you need to know that we drugged and brainwashed him. Almost all of his thoughts and instincts are that of a trained animal, and he is under orders of my mistress because she tricked him into thinking that she is his friend and that you are his enemies."_

_"We infused his system with a drug that will turn any flashes of recognition of you and your team and twist them so that he believes you are the ones that tortured him for a month."_

"Well, that would explain why he's cowering under a desk right now."

_"Yes. But I'm out of time now and must go but do me a favor an take care of him. He responds to the name Jay and what ever you do, don't give him any painkillers or sedatives, it'll react with our drug and cause severe brain damage!"_ Elizabeth was in shock as the line went dead, she quickly turned to see Rodney and Teyla struggling to hold on to the flailing major and Beckett preparing a sedative for him.

"Carson, stop!" The three looked up at her in surprise.

"What's wrong, lassie?"

"Don't give him that, just hold him there while I order a stretcher. We can't give him any sedatives or painmeds, it could harm his health." They all looked at her like she was insane but stayed quiet but held him firm as she walked slowly over to them. Kneeling down, Elizabeth smiled softly at John,who panting desperately for breath to fight against the pain in his side.

"It's alright, Jay, calm down." Rodney, Carson and Teyla raised an eyebrow at her but she simply continued talking quietly as she reached her hand out towards the major's head, "Wuna contacted me and told me to take care of you but you got cooperate with us. I know you're scared and think that we did all those horrible things to you but you don't have to be afraid anymore, we're gonna help you with the pain in your side." John shut his eyes in fear as she placed her hand on his hair, but calmed the tiniest bit as she petted his hair gently the way Thuqua did.

"Elizabeth, have you gone batty!" Rodney hissed as they heard the med team coming.

"Quiet Rodney, he's really messed up. Just treat him like you would a scared pet." She motioned for them to place him on the ground, he lay still except for the shivers of terror as Beckett was finally able to take care of the wound.

~~~~~A/N: Sorry, this chapter felt a little rushed... R&R please.


End file.
